Transcriptomic profiling and regulatory pathway modeling in a renal allograft transplantation model

Chronic allograft dysfunction (CAD) following kidney transplantation is characterized by progressive fibrosis and a smoldering inflammatory infiltrate. A modified Fischer 344 (RT1lvl) to Lewis (RT1l) rat renal allograft model was used to study transcriptomic changes during the initiation and progression of CAD and to identify potential therapeutic modes of action of treatment with 13cRA previously shown to limit the development of CAD. Transcriptomic profiling was performed using Affymetrix DNA arrays at time points 0, 7, 14 and 56 days after transplantation. The animal model showed development of significant chronic fibrotic damage with accompanying inflammatory infiltrate by day 56 after transplantation. Regulatory pathways were identified by the Database for Annotation, Visualization, and Integrated Discovery (DAVID) and modulated, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways database. Microarray analysis revealed dramatic changes in the mRNA expression levels of genes associated with inflammation and fibrosis, as well as the hedgehog and WNT pathways, with a gradual increase in the number of differentially regulated genes during progression of tissue damage. Disease phenotype, as well as differential regulation of select components of the hedgehog, canonical WNT and WNT-Ca2+ signaling pathways could be verified by quantitative PCR (qPCR) and immunohistochemistry. Treatment with 13cRA, not only attenuated disease progression, but even reversed early effects of CAD. The overall effects of the treatment are mediated by a potentially direct influence on fibrosis and inflammation associated gene expression, as well as by a specific modulation, observed for hedgehog and WNT pathway activations. The results identify a series of potential pathways that may represent therapeutic targets in chronic allograft dysfunction